Magnesium in PDB 5s4q: Tubulin-Z422344882-Complex

The structure of Tubulin-Z422344882-Complex, PDB code: 5s4q was solved by T.Muehlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	118.76 / 2.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	104.743, 158.302, 179.614, 90, 90, 90
R / Rfree (%)	22.6 / 28.2

The structure of Tubulin-Z422344882-Complex also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Magnesium atom in the Tubulin-Z422344882-Complex (pdb code 5s4q). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Tubulin-Z422344882-Complex, PDB code: 5s4q:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg502 b:45.1 occ:1.00 O A:HOH621 2.0 41.9 1.0 O1G A:GTP501 2.0 33.9 1.0 O A:HOH609 2.1 48.4 1.0 O A:HOH613 2.2 32.4 1.0 O A:HOH605 2.3 45.9 1.0 O1B A:GTP501 2.4 40.6 1.0 PG A:GTP501 3.3 45.0 1.0 OE1 A:GLU71 3.4 61.8 1.0 PB A:GTP501 3.5 41.7 1.0 NZ B:LYS254 3.8 52.3 1.0 O3B A:GTP501 3.8 54.2 1.0 O3A A:GTP501 3.9 47.4 1.0 O2G A:GTP501 3.9 40.7 1.0 NE2 A:GLN11 4.0 52.6 1.0 CB A:GLN11 4.0 46.5 1.0 OD1 A:ASP69 4.3 44.5 1.0 CB A:ASP98 4.4 43.6 1.0 OD2 A:ASP69 4.5 37.0 1.0 O1A A:GTP501 4.5 40.1 1.0 O3G A:GTP501 4.5 40.8 1.0 N A:GLN11 4.6 43.0 1.0 OD2 A:ASP98 4.6 53.0 1.0 CD A:GLU71 4.7 58.1 1.0 CG A:ASP98 4.7 49.8 1.0 PA A:GTP501 4.8 51.3 1.0 O2B A:GTP501 4.8 50.2 1.0 CG A:ASP69 4.9 45.2 1.0 CA A:GLN11 4.9 45.9 1.0 CD A:GLN11 5.0 52.1 1.0

Magnesium binding site 2 out of 5 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:34.4 occ:1.00 O B:HOH612 1.8 35.0 1.0 OE1 B:GLN11 2.0 43.6 1.0 O B:HOH635 2.3 35.8 1.0 O1A B:GDP501 2.3 35.9 1.0 O C:HOH628 2.3 34.4 1.0 CD B:GLN11 3.2 48.5 1.0 OD2 B:ASP179 3.4 45.2 1.0 PA B:GDP501 3.7 29.9 1.0 NE2 B:GLN11 4.0 58.4 1.0 CB B:GLN11 4.1 37.4 1.0 CG B:GLN11 4.2 43.3 1.0 O3A B:GDP501 4.3 34.6 1.0 O C:HOH610 4.5 45.5 1.0 OD1 B:ASN101 4.5 44.9 1.0 O1B B:GDP501 4.5 34.2 1.0 CG B:ASP179 4.6 44.4 1.0 C5' B:GDP501 4.6 40.7 1.0 OE1 C:GLU254 4.6 47.3 1.0 O2A B:GDP501 4.6 31.1 1.0 O5' B:GDP501 4.6 32.2 1.0 C8 B:GDP501 4.8 39.3 1.0 O C:HOH717 4.8 52.1 1.0

Magnesium binding site 3 out of 5 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg501 b:45.8 occ:1.00 O C:HOH660 1.8 43.8 1.0 O1B C:GTP501 2.2 39.7 1.0 O1G C:GTP501 2.3 29.9 1.0 O C:HOH601 2.8 32.2 1.0 O C:HOH604 3.0 36.0 1.0 PB C:GTP501 3.2 36.0 1.0 O3A C:GTP501 3.3 38.9 1.0 NZ D:LYS254 3.5 44.3 1.0 O1A C:GTP501 3.6 40.4 1.0 PG C:GTP501 3.6 34.6 1.0 CB C:GLN11 3.7 35.7 1.0 OE1 C:GLN11 3.8 43.6 1.0 O3B C:GTP501 3.9 44.5 1.0 PA C:GTP501 4.0 34.1 1.0 OE2 C:GLU71 4.3 49.0 1.0 O C:HOH723 4.4 64.6 1.0 CD C:GLN11 4.4 47.3 1.0 O2B C:GTP501 4.5 36.5 1.0 N C:GLN11 4.5 32.9 1.0 O2G C:GTP501 4.5 35.7 1.0 O3G C:GTP501 4.7 34.9 1.0 CG C:GLN11 4.7 39.5 1.0 CE D:LYS254 4.7 39.4 1.0 O2A C:GTP501 4.7 39.3 1.0 CA C:GLN11 4.7 39.1 1.0 O D:HOH608 4.7 54.0 1.0 OD2 C:ASP98 4.8 46.6 1.0

Magnesium binding site 4 out of 5 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg503 b:61.2 occ:1.00 OE1 D:GLN11 1.9 67.8 1.0 O D:HOH605 2.0 50.3 1.0 O1A D:GDP502 3.1 80.3 1.0 CD D:GLN11 3.1 71.9 1.0 O2A D:GDP502 3.8 61.1 1.0 NE2 D:GLN11 3.9 71.5 1.0 PA D:GDP502 4.0 59.7 1.0 O D:HOH609 4.1 65.3 1.0 CG D:GLN11 4.2 74.8 1.0 CB D:GLN11 4.3 69.8 1.0 C8 D:GDP502 4.6 63.8 1.0 C5' D:GDP502 4.7 59.7 1.0 O5' D:GDP502 4.9 57.8 1.0 O1B D:GDP502 4.9 65.0 1.0

Magnesium binding site 5 out of 5 in the Tubulin-Z422344882-Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Tubulin-Z422344882-Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:85.0 occ:1.00 O1B F:ACP401 2.1 112.8 1.0 O3G F:ACP401 2.3 108.5 1.0 OE2 F:GLU331 2.7 98.3 1.0 OE1 F:GLU331 3.2 102.2 1.0 PB F:ACP401 3.2 118.0 1.0 CD F:GLU331 3.3 98.0 1.0 O2B F:ACP401 3.4 112.9 1.0 OD1 F:ASN333 3.6 99.3 1.0 NZ F:LYS74 3.6 103.0 1.0 PG F:ACP401 3.7 128.2 1.0 C3B F:ACP401 4.1 109.4 1.0 O1G F:ACP401 4.5 120.6 1.0 O3A F:ACP401 4.5 109.5 1.0 CG F:ASN333 4.6 91.8 1.0 CE F:LYS74 4.7 96.7 1.0 O2G F:ACP401 4.8 101.0 1.0 CG F:GLU331 4.8 87.1 1.0 O1A F:ACP401 4.9 100.9 1.0

T.Muhlethaler, D.Gioia, A.E.Prota, M.E.Sharpe, A.Cavalli, M.O.Steinmetz. Comprehensive Analysis of Binding Sites in Tubulin. Angew.Chem.Int.Ed.Engl. V. 60 13331 2021.
ISSN: ESSN 1521-3773
PubMed: 33951246
DOI: 10.1002/ANIE.202100273